Originally Posted by LightingGuy
Speculating, correct me if I'm wrong.........
Someone at AA told me once that even though both airlines use Sabre, AS uses a less extensive version that doesn't allow them to assign different FF plan numbers to segments. AA agents are able to do this. This way if you purchase a ticket with both AA and AS flights on the same ticket, you can split the miles between the two programs. I don't know how or if this affects the OP's issue though.
FWIW, the problem happens in the other direction, too. I had a flight last week SEA-LAX-AUS, then AUS-SJC-SEA. The LAX-AUS and AUS-SJC segments were on AA, the SEA-LAX, SJC-SEA were on AS. I booked the ticket on alaskaair.com. I tried to get AA to change my FF number on the AA segments so I could request an upgrade and they said they couldn't because it was on AS ticket stock. I could only do it at the airport the day of the flight after I had checked in.